Skill OpenCode
Build enhancer-driven gene regulatory networks (eRegulons) from paired scRNA+scATAC multiome data using SCENIC+, with a FigR alternative in R.
not rated 115 3mo ago A 44 tokens
Skill OpenCode
Normalize raw RNA-seq count matrices: pre-filter genes, estimate between-sample size factors (RLE/TMM), compute TPM, variance-stabilize for visualization, correct GC/length bias, and normalize single-cell data.
not rated 115 3mo ago A 51 tokens
Skill OpenCode
Annotate ChIP-seq / ATAC-seq peaks with gene features, ENCODE cCRE regulatory classes, and gene-set enrichment using ChIPseeker, HOMER, rGREAT, and ChIP-Enrich.
not rated 115 3mo ago A 53 tokens
Skill OpenCode
Analyze a single-cell pooled CRISPR perturbation screen: assign sgRNAs to cells, filter escapers via Mixscape, fit per-gene differential expression (SCEPTRE/PyDESeq2), and rank perturbations by molecular effect.
not rated 115 3mo ago A 58 tokens
Skill OpenCode
Analyze Perturb-seq CRISPR screens by linking guide RNA assignments to single-cell transcriptional phenotypes using pertpy and Seurat Mixscape.
not rated 115 3mo ago A 38 tokens
Skill OpenCode
Assign cell types to segmented IMC single cells from protein marker expression via Leiden clustering, manual gating, or SOM/supervised classification.
not rated 115 3mo ago A 33 tokens
Skill OpenCode
Preprocess scRNA-seq data: QC metrics, filtering, normalization, highly variable gene selection, and scaling for downstream analysis. Covers Scanpy (Python) and Seurat (R).
not rated 115 3mo ago A 43 tokens
Skill OpenCode
Analyze single-cell ATAC-seq data: QC, LSI dimensionality reduction, clustering, peak calling, and motif activity scoring.
not rated 115 3mo ago A 34 tokens
Skill OpenCode
Infer transcription factor regulons from scRNA-seq with the pySCENIC three-step pipeline (GRNBoost2 → cisTarget → AUCell) plus downstream interpretation.
not rated 115 3mo ago A 44 tokens
Skill OpenCode
Analyze single-cell TCR/BCR immune receptor data with scRNA-seq gene expression using scirpy for joint clonotype and cell-state analysis.
not rated 115 3mo ago A 37 tokens
Skill OpenCode
Complete single-cell RNA-seq workflow from 10X Cell Ranger counts to annotated cell types, with parallel Seurat (R) and scanpy (Python) paths.
not rated 115 3mo ago A 43 tokens
Skill OpenCode
Process 10X scATAC / Multiome data from cellranger output to clustered, annotated cells with per-cluster peaks; choose Signac / ArchR / SnapATAC2 by language and scale.
not rated 115 3mo ago A 50 tokens
Skill OpenCode
Detect and remove doublets from scRNA-seq data using Scrublet, DoubletFinder, or scDblFinder.
not rated 115 3mo ago A 35 tokens
Skill OpenCode
Single-cell alternative splicing analysis: chemistry gating, junction quantification, per-cell PSI estimation with modality classification, differential splicing / cell-state association testing, APA pivot for 10X 3' data, and quality control with failure-mode reconciliation.
not rated 115 3mo ago A 57 tokens
Skill OpenCode
Memory-efficient storage, manipulation, and normalization of zero-heavy (single-cell) expression matrices using scipy.sparse and AnnData.
not rated 115 3mo ago A 32 tokens
Skill OpenCode
Analyze spatial cell-cell interactions in multiplexed imaging (IMC) data using squidpy: build spatial neighborhood graphs, test interaction enrichment, characterize local microenvironments, identify spatial domains, and visualize/export results.
not rated 115 3mo ago A 48 tokens
Skill OpenCode
Estimate cell-type composition in spatial transcriptomics spots using an annotated scRNA-seq reference (cell2location primary; Tangram and RCTD alternatives).
not rated 115 3mo ago A 39 tokens
Skill OpenCode
Identify spatial domains (tissue regions) in spatial transcriptomics data by combining gene expression with spatial proximity, then refine, evaluate, and annotate them.
not rated 115 3mo ago A 37 tokens
Skill OpenCode
Visualize spatial transcriptomics data: overlay gene expression, clusters, QC metrics, and spatial statistics on tissue coordinates with optional histology background, interactive napari views, and publication-quality figures.
not rated 115 3mo ago A 46 tokens
Skill OpenCode
Download and verify FASTQ from SRA/ENA accessions, with metadata resolution, single-cell/10x technical-read handling, and cloud (STRIDES) support.
not rated 115 3mo ago A 40 tokens
Skill OpenCode
Profile RBP-RNA targets without UV crosslinking or immunoprecipitation using deaminase-RBP fusions (STAMP/TRIBE/DART-seq); recover RBP-specific editing sites computationally from bulk RNA-seq or scRNA-seq by subtracting a deaminase-only control.
not rated 115 3mo ago A 70 tokens
Skill OpenCode
End-to-end TCR/BCR repertoire analysis from FASTQ to clonotype diversity metrics. Use when analyzing immune repertoire sequencing data from bulk or single-cell experiments.
not rated 115 3mo ago A 39 tokens
Skill OpenCode
Infer developmental trajectories and pseudotime ordering from single-cell data using Monocle3, Slingshot, scVelo, PAGA, and velocyto.
not rated 115 3mo ago A 40 tokens
Skill OpenCode
Fit smooth non-linear curves to gene expression time series using GAMs (mgcv/tradeSeq), test for temporal trends and condition differences, detect abrupt changepoints (segmented/ruptures), and visualize fitted trajectories with confidence intervals.
not rated 115 3mo ago A 55 tokens
At most 3 mods per repository are shown here, and a mod shipped inside a plugin is left to that plugin's page — the rest are on their repository pages: